Multiple sequence alignment - TraesCS5A01G063000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5A01G063000 chr5A 100.000 2683 0 0 1 2683 68552311 68549629 0.000000e+00 4955.0
1 TraesCS5A01G063000 chr5A 100.000 37 0 0 2 38 477454931 477454895 4.790000e-08 69.4
2 TraesCS5A01G063000 chr5D 89.734 1880 96 51 844 2683 73400166 73398344 0.000000e+00 2313.0
3 TraesCS5A01G063000 chr5D 86.486 1036 65 39 620 1598 73464980 73463963 0.000000e+00 1068.0
4 TraesCS5A01G063000 chr5D 95.767 189 7 1 392 579 73465420 73465232 1.210000e-78 303.0
5 TraesCS5A01G063000 chr5D 86.312 263 24 8 416 676 73407604 73407352 2.630000e-70 276.0
6 TraesCS5A01G063000 chr5D 90.435 115 8 3 680 794 73407265 73407154 5.980000e-32 148.0
7 TraesCS5A01G063000 chr5B 85.628 988 47 46 915 1867 81194754 81193827 0.000000e+00 950.0
8 TraesCS5A01G063000 chr5B 89.177 693 59 7 2003 2683 81193805 81193117 0.000000e+00 850.0
9 TraesCS5A01G063000 chr5B 85.742 519 43 19 416 920 81195487 81194986 1.100000e-143 520.0
10 TraesCS5A01G063000 chr5B 86.732 407 34 11 1418 1820 711573390 711573000 4.100000e-118 435.0
11 TraesCS5A01G063000 chr5B 85.091 275 13 7 119 393 81195799 81195553 3.430000e-64 255.0
12 TraesCS5A01G063000 chr7A 86.978 407 33 10 1418 1820 12398582 12398972 8.820000e-120 440.0
13 TraesCS5A01G063000 chr7A 90.530 264 22 2 2420 2683 522495212 522495472 1.980000e-91 346.0
14 TraesCS5A01G063000 chr7A 97.619 42 1 0 1 42 683751376 683751417 3.710000e-09 73.1
15 TraesCS5A01G063000 chr7D 88.496 226 18 4 1572 1793 60613736 60613515 1.580000e-67 267.0
16 TraesCS5A01G063000 chr7D 90.476 84 6 2 1418 1501 60613825 60613744 2.820000e-20 110.0
17 TraesCS5A01G063000 chr2B 100.000 39 0 0 1 39 363745264 363745302 3.710000e-09 73.1
18 TraesCS5A01G063000 chr2B 100.000 38 0 0 1 38 526997179 526997142 1.330000e-08 71.3
19 TraesCS5A01G063000 chr3D 100.000 38 0 0 1 38 11469576 11469613 1.330000e-08 71.3
20 TraesCS5A01G063000 chr3D 95.122 41 2 0 1 41 84506021 84505981 6.200000e-07 65.8
21 TraesCS5A01G063000 chr2A 100.000 38 0 0 1 38 632408460 632408497 1.330000e-08 71.3
22 TraesCS5A01G063000 chr3A 91.837 49 3 1 1 48 16940408 16940456 1.720000e-07 67.6
23 TraesCS5A01G063000 chr1D 95.238 42 2 0 1 42 494455832 494455791 1.720000e-07 67.6


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G063000 chr5A 68549629 68552311 2682 True 4955.00 4955 100.0000 1 2683 1 chr5A.!!$R1 2682
1 TraesCS5A01G063000 chr5D 73398344 73400166 1822 True 2313.00 2313 89.7340 844 2683 1 chr5D.!!$R1 1839
2 TraesCS5A01G063000 chr5D 73463963 73465420 1457 True 685.50 1068 91.1265 392 1598 2 chr5D.!!$R3 1206
3 TraesCS5A01G063000 chr5B 81193117 81195799 2682 True 643.75 950 86.4095 119 2683 4 chr5B.!!$R2 2564

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
89 90 0.109086 CTACTGCACTCACCGACCAG 60.109 60.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1879 2458 1.202099 TGGGCCCGGATGAAGTAACA 61.202 55.0 19.37 0.0 0.0 2.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.898002 GGACGTCCGTTTAGGGTC 57.102 61.111 20.85 0.00 41.52 4.46
20 21 1.153958 GGACGTCCGTTTAGGGTCG 60.154 63.158 20.85 6.58 41.52 4.79
21 22 1.803117 GACGTCCGTTTAGGGTCGC 60.803 63.158 3.51 0.00 41.52 5.19
22 23 2.877582 CGTCCGTTTAGGGTCGCG 60.878 66.667 0.00 0.00 41.52 5.87
23 24 3.184003 GTCCGTTTAGGGTCGCGC 61.184 66.667 0.00 0.00 41.52 6.86
24 25 4.781959 TCCGTTTAGGGTCGCGCG 62.782 66.667 26.76 26.76 41.52 6.86
27 28 3.484547 GTTTAGGGTCGCGCGGTG 61.485 66.667 31.69 1.17 0.00 4.94
28 29 3.682885 TTTAGGGTCGCGCGGTGA 61.683 61.111 31.69 8.02 0.00 4.02
29 30 3.223710 TTTAGGGTCGCGCGGTGAA 62.224 57.895 31.69 14.18 0.00 3.18
30 31 3.636313 TTAGGGTCGCGCGGTGAAG 62.636 63.158 31.69 0.00 0.00 3.02
33 34 4.072088 GGTCGCGCGGTGAAGTTG 62.072 66.667 31.69 0.00 0.00 3.16
34 35 4.072088 GTCGCGCGGTGAAGTTGG 62.072 66.667 31.69 0.00 0.00 3.77
38 39 3.726517 CGCGGTGAAGTTGGCCTG 61.727 66.667 3.32 0.00 0.00 4.85
39 40 2.281484 GCGGTGAAGTTGGCCTGA 60.281 61.111 3.32 0.00 0.00 3.86
40 41 1.675641 GCGGTGAAGTTGGCCTGAT 60.676 57.895 3.32 0.00 0.00 2.90
41 42 1.244019 GCGGTGAAGTTGGCCTGATT 61.244 55.000 3.32 0.00 0.00 2.57
42 43 0.804989 CGGTGAAGTTGGCCTGATTC 59.195 55.000 3.32 5.87 0.00 2.52
43 44 1.177401 GGTGAAGTTGGCCTGATTCC 58.823 55.000 3.32 0.10 0.00 3.01
44 45 1.547675 GGTGAAGTTGGCCTGATTCCA 60.548 52.381 3.32 0.00 0.00 3.53
45 46 2.450476 GTGAAGTTGGCCTGATTCCAT 58.550 47.619 3.32 0.00 32.92 3.41
46 47 2.827921 GTGAAGTTGGCCTGATTCCATT 59.172 45.455 3.32 0.00 32.92 3.16
47 48 3.259123 GTGAAGTTGGCCTGATTCCATTT 59.741 43.478 3.32 0.00 32.92 2.32
48 49 3.903090 TGAAGTTGGCCTGATTCCATTTT 59.097 39.130 3.32 0.00 32.92 1.82
49 50 5.047377 GTGAAGTTGGCCTGATTCCATTTTA 60.047 40.000 3.32 0.00 32.92 1.52
50 51 5.047377 TGAAGTTGGCCTGATTCCATTTTAC 60.047 40.000 3.32 0.00 32.92 2.01
51 52 3.769300 AGTTGGCCTGATTCCATTTTACC 59.231 43.478 3.32 0.00 32.92 2.85
52 53 2.374184 TGGCCTGATTCCATTTTACCG 58.626 47.619 3.32 0.00 0.00 4.02
53 54 1.067060 GGCCTGATTCCATTTTACCGC 59.933 52.381 0.00 0.00 0.00 5.68
54 55 1.268539 GCCTGATTCCATTTTACCGCG 60.269 52.381 0.00 0.00 0.00 6.46
55 56 2.014128 CCTGATTCCATTTTACCGCGT 58.986 47.619 4.92 0.00 0.00 6.01
56 57 2.031683 CCTGATTCCATTTTACCGCGTC 59.968 50.000 4.92 0.00 0.00 5.19
57 58 1.661617 TGATTCCATTTTACCGCGTCG 59.338 47.619 4.92 0.00 0.00 5.12
58 59 1.662122 GATTCCATTTTACCGCGTCGT 59.338 47.619 4.92 0.00 0.00 4.34
59 60 1.070038 TTCCATTTTACCGCGTCGTC 58.930 50.000 4.92 0.00 0.00 4.20
60 61 0.244450 TCCATTTTACCGCGTCGTCT 59.756 50.000 4.92 0.00 0.00 4.18
61 62 1.073177 CCATTTTACCGCGTCGTCTT 58.927 50.000 4.92 0.00 0.00 3.01
62 63 1.060122 CCATTTTACCGCGTCGTCTTC 59.940 52.381 4.92 0.00 0.00 2.87
63 64 1.722464 CATTTTACCGCGTCGTCTTCA 59.278 47.619 4.92 0.00 0.00 3.02
64 65 1.411394 TTTTACCGCGTCGTCTTCAG 58.589 50.000 4.92 0.00 0.00 3.02
65 66 0.387622 TTTACCGCGTCGTCTTCAGG 60.388 55.000 4.92 0.00 0.00 3.86
66 67 2.807631 TTACCGCGTCGTCTTCAGGC 62.808 60.000 4.92 0.00 0.00 4.85
71 72 4.070552 GTCGTCTTCAGGCGCCCT 62.071 66.667 26.15 7.86 0.00 5.19
72 73 2.361992 TCGTCTTCAGGCGCCCTA 60.362 61.111 26.15 8.91 29.64 3.53
73 74 2.202756 CGTCTTCAGGCGCCCTAC 60.203 66.667 26.15 13.26 29.64 3.18
74 75 2.711922 CGTCTTCAGGCGCCCTACT 61.712 63.158 26.15 0.00 29.64 2.57
75 76 1.153549 GTCTTCAGGCGCCCTACTG 60.154 63.158 26.15 15.69 36.07 2.74
76 77 2.512515 CTTCAGGCGCCCTACTGC 60.513 66.667 26.15 0.00 34.76 4.40
77 78 3.315142 CTTCAGGCGCCCTACTGCA 62.315 63.158 26.15 3.85 34.76 4.41
78 79 3.605749 TTCAGGCGCCCTACTGCAC 62.606 63.158 26.15 0.00 34.76 4.57
79 80 4.087892 CAGGCGCCCTACTGCACT 62.088 66.667 26.15 0.00 29.64 4.40
80 81 3.775654 AGGCGCCCTACTGCACTC 61.776 66.667 26.15 0.00 28.47 3.51
81 82 4.082523 GGCGCCCTACTGCACTCA 62.083 66.667 18.11 0.00 0.00 3.41
82 83 2.815647 GCGCCCTACTGCACTCAC 60.816 66.667 0.00 0.00 0.00 3.51
83 84 2.125512 CGCCCTACTGCACTCACC 60.126 66.667 0.00 0.00 0.00 4.02
84 85 2.125512 GCCCTACTGCACTCACCG 60.126 66.667 0.00 0.00 0.00 4.94
85 86 2.646175 GCCCTACTGCACTCACCGA 61.646 63.158 0.00 0.00 0.00 4.69
86 87 1.215647 CCCTACTGCACTCACCGAC 59.784 63.158 0.00 0.00 0.00 4.79
87 88 1.215647 CCTACTGCACTCACCGACC 59.784 63.158 0.00 0.00 0.00 4.79
88 89 1.532604 CCTACTGCACTCACCGACCA 61.533 60.000 0.00 0.00 0.00 4.02
89 90 0.109086 CTACTGCACTCACCGACCAG 60.109 60.000 0.00 0.00 0.00 4.00
90 91 2.154798 TACTGCACTCACCGACCAGC 62.155 60.000 0.00 0.00 0.00 4.85
91 92 4.314440 TGCACTCACCGACCAGCC 62.314 66.667 0.00 0.00 0.00 4.85
93 94 3.680786 CACTCACCGACCAGCCGA 61.681 66.667 0.00 0.00 0.00 5.54
94 95 3.374402 ACTCACCGACCAGCCGAG 61.374 66.667 0.00 0.00 0.00 4.63
95 96 4.135153 CTCACCGACCAGCCGAGG 62.135 72.222 0.00 0.00 0.00 4.63
99 100 4.697756 CCGACCAGCCGAGGCAAA 62.698 66.667 17.18 0.00 44.88 3.68
100 101 2.668212 CGACCAGCCGAGGCAAAA 60.668 61.111 17.18 0.00 44.88 2.44
101 102 2.954611 GACCAGCCGAGGCAAAAC 59.045 61.111 17.18 1.60 44.88 2.43
102 103 2.966309 GACCAGCCGAGGCAAAACG 61.966 63.158 17.18 1.06 44.88 3.60
103 104 4.404654 CCAGCCGAGGCAAAACGC 62.405 66.667 17.18 0.00 44.88 4.84
104 105 4.741781 CAGCCGAGGCAAAACGCG 62.742 66.667 17.18 3.53 44.88 6.01
106 107 4.322385 GCCGAGGCAAAACGCGTT 62.322 61.111 20.79 20.79 43.84 4.84
107 108 2.330041 CCGAGGCAAAACGCGTTT 59.670 55.556 30.36 30.36 43.84 3.60
108 109 1.570475 CCGAGGCAAAACGCGTTTA 59.430 52.632 34.89 0.00 43.84 2.01
109 110 0.167251 CCGAGGCAAAACGCGTTTAT 59.833 50.000 34.89 22.16 43.84 1.40
110 111 1.400500 CCGAGGCAAAACGCGTTTATT 60.400 47.619 34.89 19.66 43.84 1.40
111 112 1.902504 CGAGGCAAAACGCGTTTATTC 59.097 47.619 34.89 25.44 43.84 1.75
112 113 1.902504 GAGGCAAAACGCGTTTATTCG 59.097 47.619 34.89 23.56 43.84 3.34
113 114 1.264826 AGGCAAAACGCGTTTATTCGT 59.735 42.857 34.89 23.45 43.84 3.85
115 116 3.059051 AGGCAAAACGCGTTTATTCGTTA 60.059 39.130 34.89 0.00 46.56 3.18
116 117 3.847457 GGCAAAACGCGTTTATTCGTTAT 59.153 39.130 34.89 15.92 46.56 1.89
117 118 4.321480 GGCAAAACGCGTTTATTCGTTATT 59.679 37.500 34.89 15.19 46.56 1.40
135 136 1.448985 TTTACCGTGCAGATCCAAGC 58.551 50.000 0.00 0.00 0.00 4.01
161 162 3.702048 TGGCTTTCCGGCGCTACT 61.702 61.111 7.64 0.00 42.02 2.57
162 163 2.436115 GGCTTTCCGGCGCTACTT 60.436 61.111 7.64 0.00 0.00 2.24
163 164 2.038837 GGCTTTCCGGCGCTACTTT 61.039 57.895 7.64 0.00 0.00 2.66
164 165 0.741927 GGCTTTCCGGCGCTACTTTA 60.742 55.000 7.64 0.00 0.00 1.85
165 166 1.081094 GCTTTCCGGCGCTACTTTAA 58.919 50.000 7.64 0.00 0.00 1.52
166 167 1.669265 GCTTTCCGGCGCTACTTTAAT 59.331 47.619 7.64 0.00 0.00 1.40
182 183 4.083484 ACTTTAATTTGCTACGTGTCCAGC 60.083 41.667 0.00 0.00 38.31 4.85
187 188 2.490217 CTACGTGTCCAGCTCCCG 59.510 66.667 0.00 0.00 0.00 5.14
193 194 1.070786 TGTCCAGCTCCCGACAAAC 59.929 57.895 5.53 0.00 36.10 2.93
198 199 1.080025 AGCTCCCGACAAACGCTAC 60.080 57.895 0.00 0.00 41.07 3.58
199 200 1.080025 GCTCCCGACAAACGCTACT 60.080 57.895 0.00 0.00 41.07 2.57
200 201 1.077089 GCTCCCGACAAACGCTACTC 61.077 60.000 0.00 0.00 41.07 2.59
201 202 0.526662 CTCCCGACAAACGCTACTCT 59.473 55.000 0.00 0.00 41.07 3.24
202 203 0.963962 TCCCGACAAACGCTACTCTT 59.036 50.000 0.00 0.00 41.07 2.85
203 204 1.068474 CCCGACAAACGCTACTCTTG 58.932 55.000 0.00 0.00 41.07 3.02
204 205 1.604693 CCCGACAAACGCTACTCTTGT 60.605 52.381 0.00 0.00 41.07 3.16
205 206 2.352030 CCCGACAAACGCTACTCTTGTA 60.352 50.000 0.00 0.00 41.07 2.41
206 207 2.660236 CCGACAAACGCTACTCTTGTAC 59.340 50.000 0.00 0.00 41.07 2.90
207 208 3.562505 CGACAAACGCTACTCTTGTACT 58.437 45.455 0.00 0.00 33.53 2.73
208 209 3.361053 CGACAAACGCTACTCTTGTACTG 59.639 47.826 0.00 0.00 33.53 2.74
209 210 4.296690 GACAAACGCTACTCTTGTACTGT 58.703 43.478 0.00 0.00 33.53 3.55
210 211 5.443185 ACAAACGCTACTCTTGTACTGTA 57.557 39.130 0.00 0.00 31.63 2.74
222 223 7.104939 ACTCTTGTACTGTACTACTAGGAGTG 58.895 42.308 18.50 3.52 0.00 3.51
228 229 5.184711 ACTGTACTACTAGGAGTGCTGTAC 58.815 45.833 26.90 14.28 40.59 2.90
229 230 5.045724 ACTGTACTACTAGGAGTGCTGTACT 60.046 44.000 26.90 9.22 40.59 2.73
230 231 6.155910 ACTGTACTACTAGGAGTGCTGTACTA 59.844 42.308 26.90 6.27 40.59 1.82
231 232 6.344500 TGTACTACTAGGAGTGCTGTACTAC 58.656 44.000 22.07 8.79 40.53 2.73
241 242 2.223377 GTGCTGTACTACTTGCAACCAC 59.777 50.000 0.00 0.00 37.17 4.16
257 258 3.452755 ACCACGCATGATTCGATTCTA 57.547 42.857 8.63 0.00 0.00 2.10
258 259 3.123804 ACCACGCATGATTCGATTCTAC 58.876 45.455 8.63 0.00 0.00 2.59
322 323 4.985538 TGAAATCTTTAGGTGTGGCTCTT 58.014 39.130 0.00 0.00 0.00 2.85
340 341 4.693095 GCTCTTGCTTAGCTTAGTTCTTGT 59.307 41.667 5.60 0.00 37.01 3.16
482 526 3.790416 TTTTCCTGGCGTGGCAGCT 62.790 57.895 17.19 0.00 37.29 4.24
540 585 5.348997 CGGAGAACAGATTCTAACCTTTCAC 59.651 44.000 0.00 0.00 45.60 3.18
559 604 5.808366 TCACTGTCACTCCTAGTCAATTT 57.192 39.130 0.00 0.00 0.00 1.82
574 619 1.135575 CAATTTCAGAGGACTTGCGCC 60.136 52.381 4.18 0.00 0.00 6.53
646 902 4.502962 GCTGAGCTAGTTGATTTCAGACT 58.497 43.478 0.00 0.00 37.96 3.24
672 928 2.359531 CCGGCAAAGTTAGGACACAAAA 59.640 45.455 0.00 0.00 0.00 2.44
678 934 7.036829 GGCAAAGTTAGGACACAAAACTAAAA 58.963 34.615 0.00 0.00 33.24 1.52
729 985 2.550830 ACTCGTGGCATTCTCTTTGT 57.449 45.000 0.00 0.00 0.00 2.83
730 986 3.678056 ACTCGTGGCATTCTCTTTGTA 57.322 42.857 0.00 0.00 0.00 2.41
731 987 3.326747 ACTCGTGGCATTCTCTTTGTAC 58.673 45.455 0.00 0.00 0.00 2.90
777 1033 2.289569 TGATTTGGGCAAAGCATTCACC 60.290 45.455 0.00 0.00 41.15 4.02
837 1104 0.884514 TCTGTGAGTGCGAGAGGAAG 59.115 55.000 0.00 0.00 0.00 3.46
838 1105 0.884514 CTGTGAGTGCGAGAGGAAGA 59.115 55.000 0.00 0.00 0.00 2.87
839 1106 1.270826 CTGTGAGTGCGAGAGGAAGAA 59.729 52.381 0.00 0.00 0.00 2.52
840 1107 1.686587 TGTGAGTGCGAGAGGAAGAAA 59.313 47.619 0.00 0.00 0.00 2.52
841 1108 2.062519 GTGAGTGCGAGAGGAAGAAAC 58.937 52.381 0.00 0.00 0.00 2.78
904 1172 0.744771 GAAACCATGTCCTCCGGCTC 60.745 60.000 0.00 0.00 0.00 4.70
933 1438 1.399089 CGTAATAAACAGCAACCCGGG 59.601 52.381 22.25 22.25 0.00 5.73
945 1450 2.618559 GCAACCCGGGGTACTAAAATCA 60.619 50.000 27.92 0.00 33.12 2.57
1035 1554 1.322637 CTCATTCATCACTCGCACACG 59.677 52.381 0.00 0.00 42.01 4.49
1055 1582 3.572255 ACGAAGCTCTCAAGAAGAAGTCT 59.428 43.478 0.00 0.00 38.69 3.24
1104 1657 1.738099 CAAGAGCCCACCTTCGTCG 60.738 63.158 0.00 0.00 0.00 5.12
1580 2151 9.054922 GTATTTGTGGTAGAGTAGGAGTACTAG 57.945 40.741 0.00 0.00 39.78 2.57
1582 2153 7.739995 TTGTGGTAGAGTAGGAGTACTAGTA 57.260 40.000 0.00 0.00 39.78 1.82
1583 2154 7.739995 TGTGGTAGAGTAGGAGTACTAGTAA 57.260 40.000 3.61 0.00 39.78 2.24
1584 2155 8.329346 TGTGGTAGAGTAGGAGTACTAGTAAT 57.671 38.462 3.61 2.68 39.78 1.89
1585 2156 8.776119 TGTGGTAGAGTAGGAGTACTAGTAATT 58.224 37.037 3.61 0.00 39.78 1.40
1586 2157 9.271828 GTGGTAGAGTAGGAGTACTAGTAATTC 57.728 40.741 3.61 1.72 39.78 2.17
1587 2158 8.996655 TGGTAGAGTAGGAGTACTAGTAATTCA 58.003 37.037 11.11 0.00 39.78 2.57
1633 2205 1.604278 GGATGCAAGGAATAACCGAGC 59.396 52.381 0.00 0.00 44.74 5.03
1636 2208 2.083774 TGCAAGGAATAACCGAGCTTG 58.916 47.619 0.00 0.00 44.74 4.01
1690 2268 2.163010 GTCAGGTGTGATGGCAAGAATG 59.837 50.000 0.00 0.00 34.36 2.67
1711 2289 3.691118 TGAAAATCAGCTCATTTCTCGGG 59.309 43.478 0.00 0.00 34.84 5.14
1726 2304 3.441101 TCTCGGGAGAAATCTTCCTTCA 58.559 45.455 6.20 0.00 39.61 3.02
1733 2311 4.019771 GGAGAAATCTTCCTTCAGTGTCCT 60.020 45.833 0.00 0.00 0.00 3.85
1734 2312 4.904241 AGAAATCTTCCTTCAGTGTCCTG 58.096 43.478 0.00 0.00 40.25 3.86
1793 2372 5.337578 AAGTTGCAACTTGCTTAGGAAAA 57.662 34.783 37.28 0.00 46.80 2.29
1794 2373 5.535753 AGTTGCAACTTGCTTAGGAAAAT 57.464 34.783 26.36 0.00 45.31 1.82
1795 2374 6.648879 AGTTGCAACTTGCTTAGGAAAATA 57.351 33.333 26.36 0.00 45.31 1.40
1796 2375 7.049799 AGTTGCAACTTGCTTAGGAAAATAA 57.950 32.000 26.36 0.00 45.31 1.40
1797 2376 7.496747 AGTTGCAACTTGCTTAGGAAAATAAA 58.503 30.769 26.36 0.00 45.31 1.40
1798 2377 7.984617 AGTTGCAACTTGCTTAGGAAAATAAAA 59.015 29.630 26.36 0.00 45.31 1.52
1799 2378 8.773645 GTTGCAACTTGCTTAGGAAAATAAAAT 58.226 29.630 22.36 0.00 45.31 1.82
1800 2379 8.532977 TGCAACTTGCTTAGGAAAATAAAATC 57.467 30.769 14.78 0.00 45.31 2.17
1801 2380 7.602265 TGCAACTTGCTTAGGAAAATAAAATCC 59.398 33.333 14.78 0.00 45.31 3.01
1804 2383 7.892609 ACTTGCTTAGGAAAATAAAATCCGTT 58.107 30.769 0.00 0.00 40.78 4.44
1823 2402 4.365723 CGTTGGTGGGTATATACACTGAC 58.634 47.826 16.00 6.84 37.72 3.51
1826 2405 3.386726 TGGTGGGTATATACACTGACTGC 59.613 47.826 16.00 0.00 37.72 4.40
1830 2409 5.293569 GTGGGTATATACACTGACTGCAAAC 59.706 44.000 16.00 0.00 34.84 2.93
1837 2416 1.472082 CACTGACTGCAAACACCACAA 59.528 47.619 0.00 0.00 0.00 3.33
1838 2417 1.745087 ACTGACTGCAAACACCACAAG 59.255 47.619 0.00 0.00 0.00 3.16
1851 2430 5.121221 ACACCACAAGCATTAAACTAAGC 57.879 39.130 0.00 0.00 0.00 3.09
1879 2458 5.091552 TCTAGACTGTTCCAATGGGTAACT 58.908 41.667 0.00 0.00 34.93 2.24
1890 2469 6.177610 TCCAATGGGTAACTGTTACTTCATC 58.822 40.000 25.04 11.57 36.39 2.92
1900 2479 2.265467 TTACTTCATCCGGGCCCAGC 62.265 60.000 24.92 0.00 0.00 4.85
1914 2493 2.363683 GCCCAGCCATTATCTGATAGC 58.636 52.381 0.00 0.00 33.54 2.97
2043 2628 2.933769 GTGCAACTTACCAGACATTGC 58.066 47.619 0.00 0.00 44.66 3.56
2062 2647 6.305399 ACATTGCGATGAAGAAAACAAATACG 59.695 34.615 21.12 0.00 36.73 3.06
2063 2648 5.599359 TGCGATGAAGAAAACAAATACGA 57.401 34.783 0.00 0.00 0.00 3.43
2074 2659 2.639065 ACAAATACGATTCGCACCCAT 58.361 42.857 5.86 0.00 0.00 4.00
2178 2763 8.203485 ACAGAAACAAAAGGATAAAGCATCAAA 58.797 29.630 0.00 0.00 35.11 2.69
2214 2799 3.555527 TGCAGATCAGCTAAGCAGATT 57.444 42.857 11.68 0.00 35.03 2.40
2241 2827 7.957002 TCTTTGTAAAGGTGCCAAATCATAAA 58.043 30.769 4.67 0.00 36.67 1.40
2289 2878 7.851228 TGTCTGGATTCAAGAGTGTTACATAT 58.149 34.615 0.00 0.00 0.00 1.78
2315 2905 4.209703 CACATGTGCCAACAACTTCATTTC 59.790 41.667 13.94 0.00 40.46 2.17
2336 2927 7.591006 TTTCGTGTGGAAATCTATCTTGTAC 57.409 36.000 0.00 0.00 39.67 2.90
2348 2939 5.437060 TCTATCTTGTACAATTGGCCTTCC 58.563 41.667 9.13 0.00 0.00 3.46
2381 2974 8.556213 AGAGATATTACGAGAGAACCTCATAC 57.444 38.462 0.00 0.00 42.06 2.39
2387 2980 2.376109 GAGAGAACCTCATACGGACCA 58.624 52.381 0.00 0.00 41.58 4.02
2388 2981 2.959707 GAGAGAACCTCATACGGACCAT 59.040 50.000 0.00 0.00 41.58 3.55
2416 3009 9.449719 CTATAAGATTGTTTTGAGTGTAGGGTT 57.550 33.333 0.00 0.00 0.00 4.11
2457 3050 6.322126 AGAATCCAGTAGCCTATCTGATTCT 58.678 40.000 12.83 12.83 35.88 2.40
2475 3068 4.701651 TTCTGAAGGCAGCATATCAGAT 57.298 40.909 19.07 0.00 45.45 2.90
2480 3073 3.851458 AGGCAGCATATCAGATGACAA 57.149 42.857 0.00 0.00 34.74 3.18
2564 3157 0.609131 AACCGCCTCACCATTTCCAG 60.609 55.000 0.00 0.00 0.00 3.86
2613 3206 4.751093 TGCCGAAGATGCGCCGAA 62.751 61.111 4.18 0.00 0.00 4.30
2634 3227 5.445939 CGAAAGCTTGTATGTCCATGTACAC 60.446 44.000 0.00 0.00 31.05 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.153958 CGACCCTAAACGGACGTCC 60.154 63.158 25.28 25.28 33.16 4.79
3 4 1.803117 GCGACCCTAAACGGACGTC 60.803 63.158 7.13 7.13 35.77 4.34
4 5 2.259511 GCGACCCTAAACGGACGT 59.740 61.111 0.00 0.00 35.77 4.34
5 6 2.877582 CGCGACCCTAAACGGACG 60.878 66.667 0.00 0.00 36.19 4.79
6 7 3.184003 GCGCGACCCTAAACGGAC 61.184 66.667 12.10 0.00 33.16 4.79
7 8 4.781959 CGCGCGACCCTAAACGGA 62.782 66.667 28.94 0.00 33.16 4.69
10 11 3.484547 CACCGCGCGACCCTAAAC 61.485 66.667 34.63 0.00 0.00 2.01
11 12 3.223710 TTCACCGCGCGACCCTAAA 62.224 57.895 34.63 13.30 0.00 1.85
12 13 3.636313 CTTCACCGCGCGACCCTAA 62.636 63.158 34.63 16.17 0.00 2.69
13 14 4.124351 CTTCACCGCGCGACCCTA 62.124 66.667 34.63 11.35 0.00 3.53
16 17 4.072088 CAACTTCACCGCGCGACC 62.072 66.667 34.63 0.00 0.00 4.79
17 18 4.072088 CCAACTTCACCGCGCGAC 62.072 66.667 34.63 0.00 0.00 5.19
21 22 3.726517 CAGGCCAACTTCACCGCG 61.727 66.667 5.01 0.00 0.00 6.46
22 23 1.244019 AATCAGGCCAACTTCACCGC 61.244 55.000 5.01 0.00 0.00 5.68
23 24 0.804989 GAATCAGGCCAACTTCACCG 59.195 55.000 5.01 0.00 0.00 4.94
24 25 1.177401 GGAATCAGGCCAACTTCACC 58.823 55.000 5.01 0.00 0.00 4.02
25 26 1.909700 TGGAATCAGGCCAACTTCAC 58.090 50.000 5.01 0.00 31.13 3.18
26 27 2.905415 ATGGAATCAGGCCAACTTCA 57.095 45.000 5.01 0.00 39.21 3.02
27 28 4.541973 AAAATGGAATCAGGCCAACTTC 57.458 40.909 5.01 3.94 39.21 3.01
28 29 4.222810 GGTAAAATGGAATCAGGCCAACTT 59.777 41.667 5.01 0.00 39.21 2.66
29 30 3.769300 GGTAAAATGGAATCAGGCCAACT 59.231 43.478 5.01 0.00 39.21 3.16
30 31 3.428862 CGGTAAAATGGAATCAGGCCAAC 60.429 47.826 5.01 0.00 39.21 3.77
31 32 2.757868 CGGTAAAATGGAATCAGGCCAA 59.242 45.455 5.01 0.00 39.21 4.52
32 33 2.374184 CGGTAAAATGGAATCAGGCCA 58.626 47.619 5.01 0.00 40.24 5.36
33 34 1.067060 GCGGTAAAATGGAATCAGGCC 59.933 52.381 0.00 0.00 0.00 5.19
34 35 1.268539 CGCGGTAAAATGGAATCAGGC 60.269 52.381 0.00 0.00 0.00 4.85
35 36 2.014128 ACGCGGTAAAATGGAATCAGG 58.986 47.619 12.47 0.00 0.00 3.86
36 37 2.285602 CGACGCGGTAAAATGGAATCAG 60.286 50.000 12.47 0.00 0.00 2.90
37 38 1.661617 CGACGCGGTAAAATGGAATCA 59.338 47.619 12.47 0.00 0.00 2.57
38 39 1.662122 ACGACGCGGTAAAATGGAATC 59.338 47.619 12.47 0.00 0.00 2.52
39 40 1.662122 GACGACGCGGTAAAATGGAAT 59.338 47.619 12.47 0.00 0.00 3.01
40 41 1.070038 GACGACGCGGTAAAATGGAA 58.930 50.000 12.47 0.00 0.00 3.53
41 42 0.244450 AGACGACGCGGTAAAATGGA 59.756 50.000 12.47 0.00 0.00 3.41
42 43 1.060122 GAAGACGACGCGGTAAAATGG 59.940 52.381 12.47 0.00 0.00 3.16
43 44 1.722464 TGAAGACGACGCGGTAAAATG 59.278 47.619 12.47 0.00 0.00 2.32
44 45 1.990563 CTGAAGACGACGCGGTAAAAT 59.009 47.619 12.47 0.00 0.00 1.82
45 46 1.411394 CTGAAGACGACGCGGTAAAA 58.589 50.000 12.47 0.00 0.00 1.52
46 47 0.387622 CCTGAAGACGACGCGGTAAA 60.388 55.000 12.47 0.00 0.00 2.01
47 48 1.210931 CCTGAAGACGACGCGGTAA 59.789 57.895 12.47 0.00 0.00 2.85
48 49 2.872557 CCTGAAGACGACGCGGTA 59.127 61.111 12.47 0.00 0.00 4.02
49 50 4.719369 GCCTGAAGACGACGCGGT 62.719 66.667 12.47 0.00 0.00 5.68
54 55 2.707849 TAGGGCGCCTGAAGACGAC 61.708 63.158 28.56 5.83 34.61 4.34
55 56 2.361992 TAGGGCGCCTGAAGACGA 60.362 61.111 28.56 0.86 34.61 4.20
56 57 2.202756 GTAGGGCGCCTGAAGACG 60.203 66.667 28.56 0.00 34.61 4.18
57 58 1.153549 CAGTAGGGCGCCTGAAGAC 60.154 63.158 28.56 16.44 34.61 3.01
58 59 3.019003 GCAGTAGGGCGCCTGAAGA 62.019 63.158 28.56 4.14 34.61 2.87
59 60 2.512515 GCAGTAGGGCGCCTGAAG 60.513 66.667 28.56 13.88 34.61 3.02
60 61 3.318384 TGCAGTAGGGCGCCTGAA 61.318 61.111 28.56 8.46 34.61 3.02
61 62 4.082523 GTGCAGTAGGGCGCCTGA 62.083 66.667 28.56 12.03 38.32 3.86
62 63 4.087892 AGTGCAGTAGGGCGCCTG 62.088 66.667 28.56 18.09 45.18 4.85
63 64 3.775654 GAGTGCAGTAGGGCGCCT 61.776 66.667 28.56 15.07 45.18 5.52
64 65 4.082523 TGAGTGCAGTAGGGCGCC 62.083 66.667 21.18 21.18 45.18 6.53
65 66 2.815647 GTGAGTGCAGTAGGGCGC 60.816 66.667 0.00 0.00 44.42 6.53
66 67 2.125512 GGTGAGTGCAGTAGGGCG 60.126 66.667 0.00 0.00 36.28 6.13
67 68 2.125512 CGGTGAGTGCAGTAGGGC 60.126 66.667 0.00 0.00 0.00 5.19
68 69 1.215647 GTCGGTGAGTGCAGTAGGG 59.784 63.158 0.00 0.00 0.00 3.53
69 70 1.215647 GGTCGGTGAGTGCAGTAGG 59.784 63.158 0.00 0.00 0.00 3.18
70 71 0.109086 CTGGTCGGTGAGTGCAGTAG 60.109 60.000 0.00 0.00 0.00 2.57
71 72 1.964448 CTGGTCGGTGAGTGCAGTA 59.036 57.895 0.00 0.00 0.00 2.74
72 73 2.737180 CTGGTCGGTGAGTGCAGT 59.263 61.111 0.00 0.00 0.00 4.40
73 74 2.740055 GCTGGTCGGTGAGTGCAG 60.740 66.667 0.00 0.00 0.00 4.41
74 75 4.314440 GGCTGGTCGGTGAGTGCA 62.314 66.667 0.00 0.00 0.00 4.57
76 77 3.633094 CTCGGCTGGTCGGTGAGTG 62.633 68.421 0.00 0.00 0.00 3.51
77 78 3.374402 CTCGGCTGGTCGGTGAGT 61.374 66.667 0.00 0.00 0.00 3.41
78 79 4.135153 CCTCGGCTGGTCGGTGAG 62.135 72.222 0.00 0.00 0.00 3.51
82 83 4.697756 TTTGCCTCGGCTGGTCGG 62.698 66.667 9.65 0.00 42.51 4.79
83 84 2.668212 TTTTGCCTCGGCTGGTCG 60.668 61.111 9.65 0.00 42.51 4.79
84 85 2.954611 GTTTTGCCTCGGCTGGTC 59.045 61.111 9.65 0.00 42.51 4.02
85 86 2.978010 CGTTTTGCCTCGGCTGGT 60.978 61.111 9.65 0.00 42.51 4.00
86 87 4.404654 GCGTTTTGCCTCGGCTGG 62.405 66.667 9.65 0.00 42.51 4.85
87 88 4.741781 CGCGTTTTGCCTCGGCTG 62.742 66.667 9.65 0.00 42.08 4.85
89 90 2.446753 TAAACGCGTTTTGCCTCGGC 62.447 55.000 38.53 0.00 42.08 5.54
90 91 0.167251 ATAAACGCGTTTTGCCTCGG 59.833 50.000 38.53 0.00 42.08 4.63
91 92 1.902504 GAATAAACGCGTTTTGCCTCG 59.097 47.619 38.53 0.00 42.08 4.63
92 93 1.902504 CGAATAAACGCGTTTTGCCTC 59.097 47.619 38.53 26.18 42.08 4.70
93 94 1.264826 ACGAATAAACGCGTTTTGCCT 59.735 42.857 38.53 21.63 42.08 4.75
94 95 1.677208 ACGAATAAACGCGTTTTGCC 58.323 45.000 38.53 25.19 42.08 4.52
100 101 4.326009 ACGGTAAATAACGAATAAACGCGT 59.674 37.500 5.58 5.58 43.39 6.01
101 102 4.656989 CACGGTAAATAACGAATAAACGCG 59.343 41.667 3.53 3.53 36.70 6.01
102 103 4.431070 GCACGGTAAATAACGAATAAACGC 59.569 41.667 4.68 0.00 36.70 4.84
103 104 5.549159 TGCACGGTAAATAACGAATAAACG 58.451 37.500 4.68 0.00 39.31 3.60
104 105 6.764094 TCTGCACGGTAAATAACGAATAAAC 58.236 36.000 4.68 0.00 0.00 2.01
105 106 6.964741 TCTGCACGGTAAATAACGAATAAA 57.035 33.333 4.68 0.00 0.00 1.40
106 107 6.201425 GGATCTGCACGGTAAATAACGAATAA 59.799 38.462 4.68 0.00 0.00 1.40
107 108 5.693104 GGATCTGCACGGTAAATAACGAATA 59.307 40.000 4.68 0.00 0.00 1.75
108 109 4.510340 GGATCTGCACGGTAAATAACGAAT 59.490 41.667 4.68 0.00 0.00 3.34
109 110 3.866910 GGATCTGCACGGTAAATAACGAA 59.133 43.478 4.68 0.00 0.00 3.85
110 111 3.119065 TGGATCTGCACGGTAAATAACGA 60.119 43.478 4.68 0.00 0.00 3.85
111 112 3.191669 TGGATCTGCACGGTAAATAACG 58.808 45.455 0.00 0.00 0.00 3.18
112 113 4.495844 GCTTGGATCTGCACGGTAAATAAC 60.496 45.833 0.00 0.00 0.00 1.89
113 114 3.625764 GCTTGGATCTGCACGGTAAATAA 59.374 43.478 0.00 0.00 0.00 1.40
114 115 3.118408 AGCTTGGATCTGCACGGTAAATA 60.118 43.478 8.17 0.00 0.00 1.40
115 116 2.017049 GCTTGGATCTGCACGGTAAAT 58.983 47.619 0.00 0.00 0.00 1.40
116 117 1.003118 AGCTTGGATCTGCACGGTAAA 59.997 47.619 8.17 0.00 0.00 2.01
117 118 0.613260 AGCTTGGATCTGCACGGTAA 59.387 50.000 8.17 0.00 0.00 2.85
135 136 3.373565 GGAAAGCCACCGCCCAAG 61.374 66.667 0.00 0.00 34.57 3.61
161 162 4.069304 AGCTGGACACGTAGCAAATTAAA 58.931 39.130 10.48 0.00 42.29 1.52
162 163 3.670625 AGCTGGACACGTAGCAAATTAA 58.329 40.909 10.48 0.00 42.29 1.40
163 164 3.259064 GAGCTGGACACGTAGCAAATTA 58.741 45.455 10.48 0.00 42.29 1.40
164 165 2.076863 GAGCTGGACACGTAGCAAATT 58.923 47.619 10.48 0.00 42.29 1.82
165 166 1.676014 GGAGCTGGACACGTAGCAAAT 60.676 52.381 10.48 0.00 42.29 2.32
166 167 0.320421 GGAGCTGGACACGTAGCAAA 60.320 55.000 10.48 0.00 42.29 3.68
182 183 0.526662 AGAGTAGCGTTTGTCGGGAG 59.473 55.000 0.00 0.00 40.26 4.30
187 188 4.296690 ACAGTACAAGAGTAGCGTTTGTC 58.703 43.478 0.00 0.00 36.52 3.18
193 194 6.200665 CCTAGTAGTACAGTACAAGAGTAGCG 59.799 46.154 13.37 5.40 0.00 4.26
198 199 6.037391 GCACTCCTAGTAGTACAGTACAAGAG 59.963 46.154 13.37 10.54 0.00 2.85
199 200 5.879223 GCACTCCTAGTAGTACAGTACAAGA 59.121 44.000 13.37 0.00 0.00 3.02
200 201 5.881443 AGCACTCCTAGTAGTACAGTACAAG 59.119 44.000 13.37 4.80 0.00 3.16
201 202 5.646793 CAGCACTCCTAGTAGTACAGTACAA 59.353 44.000 13.37 0.00 0.00 2.41
202 203 5.183969 CAGCACTCCTAGTAGTACAGTACA 58.816 45.833 13.37 0.00 0.00 2.90
203 204 5.184711 ACAGCACTCCTAGTAGTACAGTAC 58.815 45.833 2.05 2.05 0.00 2.73
204 205 5.432680 ACAGCACTCCTAGTAGTACAGTA 57.567 43.478 2.52 0.00 0.00 2.74
205 206 4.304048 ACAGCACTCCTAGTAGTACAGT 57.696 45.455 2.52 0.00 0.00 3.55
206 207 5.430007 AGTACAGCACTCCTAGTAGTACAG 58.570 45.833 2.52 0.00 34.96 2.74
207 208 5.432680 AGTACAGCACTCCTAGTAGTACA 57.567 43.478 2.52 0.00 34.96 2.90
208 209 6.581712 AGTAGTACAGCACTCCTAGTAGTAC 58.418 44.000 2.52 0.00 40.84 2.73
209 210 6.805016 AGTAGTACAGCACTCCTAGTAGTA 57.195 41.667 2.52 0.00 38.80 1.82
210 211 5.697082 AGTAGTACAGCACTCCTAGTAGT 57.303 43.478 2.52 0.00 38.80 2.73
222 223 1.459592 CGTGGTTGCAAGTAGTACAGC 59.540 52.381 0.00 6.92 0.00 4.40
241 242 6.696825 ATTACTGTAGAATCGAATCATGCG 57.303 37.500 2.82 0.00 0.00 4.73
311 312 0.322008 AGCTAAGCAAGAGCCACACC 60.322 55.000 0.00 0.00 43.56 4.16
322 323 3.498397 GCACACAAGAACTAAGCTAAGCA 59.502 43.478 0.00 0.00 0.00 3.91
360 361 7.391148 TGGTCAAGCTAATTAATTTGGAGAC 57.609 36.000 5.91 8.51 0.00 3.36
482 526 4.582656 CCAGTTGGGTAAGAACACATTTCA 59.417 41.667 0.00 0.00 39.27 2.69
540 585 6.030548 TCTGAAATTGACTAGGAGTGACAG 57.969 41.667 0.00 0.00 0.00 3.51
559 604 0.898326 TAGTGGCGCAAGTCCTCTGA 60.898 55.000 10.83 0.00 45.49 3.27
588 633 3.392616 GAGAGAGAGAGAGAGAGGATGGT 59.607 52.174 0.00 0.00 0.00 3.55
589 634 3.649981 AGAGAGAGAGAGAGAGAGGATGG 59.350 52.174 0.00 0.00 0.00 3.51
590 635 4.592351 AGAGAGAGAGAGAGAGAGAGGATG 59.408 50.000 0.00 0.00 0.00 3.51
591 636 4.825445 AGAGAGAGAGAGAGAGAGAGGAT 58.175 47.826 0.00 0.00 0.00 3.24
592 637 4.271807 AGAGAGAGAGAGAGAGAGAGGA 57.728 50.000 0.00 0.00 0.00 3.71
597 643 6.630413 GCAGTTTCTAGAGAGAGAGAGAGAGA 60.630 46.154 0.00 0.00 31.77 3.10
605 651 1.746220 GCCGCAGTTTCTAGAGAGAGA 59.254 52.381 0.00 0.00 31.77 3.10
646 902 2.223745 GTCCTAACTTTGCCGGTTTCA 58.776 47.619 1.90 0.00 0.00 2.69
672 928 9.165035 TGACGACCCGAAATTATAAATTTTAGT 57.835 29.630 0.00 0.00 0.00 2.24
678 934 6.218019 TCGATGACGACCCGAAATTATAAAT 58.782 36.000 0.00 0.00 43.81 1.40
711 967 3.589988 AGTACAAAGAGAATGCCACGAG 58.410 45.455 0.00 0.00 0.00 4.18
729 985 9.688091 TTGCAAGTTAATTAATCCCATGTAGTA 57.312 29.630 0.31 0.00 0.00 1.82
730 986 8.588290 TTGCAAGTTAATTAATCCCATGTAGT 57.412 30.769 0.31 0.00 0.00 2.73
731 987 9.467258 CATTGCAAGTTAATTAATCCCATGTAG 57.533 33.333 4.94 0.00 0.00 2.74
772 1028 1.142667 TGTGGAGCACATTCAGGTGAA 59.857 47.619 0.00 0.00 39.62 3.18
777 1033 1.955778 TGGTTTGTGGAGCACATTCAG 59.044 47.619 0.00 0.00 44.16 3.02
794 1050 2.026822 GTGATGGGAGATGACTTGTGGT 60.027 50.000 0.00 0.00 0.00 4.16
795 1051 2.636830 GTGATGGGAGATGACTTGTGG 58.363 52.381 0.00 0.00 0.00 4.17
824 1080 2.910688 TTGTTTCTTCCTCTCGCACT 57.089 45.000 0.00 0.00 0.00 4.40
837 1104 9.402657 GCTTTTGTTTTTGTTTTGTTTTGTTTC 57.597 25.926 0.00 0.00 0.00 2.78
838 1105 8.925700 TGCTTTTGTTTTTGTTTTGTTTTGTTT 58.074 22.222 0.00 0.00 0.00 2.83
839 1106 8.466086 TGCTTTTGTTTTTGTTTTGTTTTGTT 57.534 23.077 0.00 0.00 0.00 2.83
840 1107 8.466086 TTGCTTTTGTTTTTGTTTTGTTTTGT 57.534 23.077 0.00 0.00 0.00 2.83
841 1108 9.192489 GTTTGCTTTTGTTTTTGTTTTGTTTTG 57.808 25.926 0.00 0.00 0.00 2.44
862 1130 4.326766 TCAGCGCCGCTTGTTTGC 62.327 61.111 9.89 0.00 36.40 3.68
914 1182 1.746787 CCCCGGGTTGCTGTTTATTAC 59.253 52.381 21.85 0.00 0.00 1.89
933 1438 8.568794 GGGAGCTCAATTATTGATTTTAGTACC 58.431 37.037 17.19 4.74 39.30 3.34
945 1450 3.288092 GGTTTCGGGGAGCTCAATTATT 58.712 45.455 17.19 0.00 0.00 1.40
1035 1554 5.132897 TCAGACTTCTTCTTGAGAGCTTC 57.867 43.478 0.00 0.00 35.37 3.86
1055 1582 1.764723 AGTCCATGGCAAGATCGATCA 59.235 47.619 26.47 7.19 0.00 2.92
1381 1946 2.366972 ATCCAGAAGGTCCGGGGG 60.367 66.667 0.00 0.00 35.89 5.40
1460 2025 2.176055 CTCGTGGTCACCGTCGAG 59.824 66.667 21.27 21.27 41.15 4.04
1537 2108 8.399425 CCACAAATACACAAACACAAGTACTAA 58.601 33.333 0.00 0.00 0.00 2.24
1633 2205 9.981114 AGGTAAATAATTTGAACAGAAACCAAG 57.019 29.630 0.00 0.00 0.00 3.61
1678 2256 5.007385 AGCTGATTTTCATTCTTGCCATC 57.993 39.130 0.00 0.00 0.00 3.51
1690 2268 3.941483 TCCCGAGAAATGAGCTGATTTTC 59.059 43.478 12.58 10.54 0.00 2.29
1711 2289 5.159273 AGGACACTGAAGGAAGATTTCTC 57.841 43.478 0.00 0.00 0.00 2.87
1733 2311 2.225343 ACCAAAATGGAGCCCTCATTCA 60.225 45.455 2.85 0.00 40.96 2.57
1734 2312 2.460669 ACCAAAATGGAGCCCTCATTC 58.539 47.619 2.85 0.00 40.96 2.67
1788 2367 4.020928 ACCCACCAACGGATTTTATTTTCC 60.021 41.667 0.00 0.00 0.00 3.13
1793 2372 7.662669 GTGTATATACCCACCAACGGATTTTAT 59.337 37.037 10.38 0.00 0.00 1.40
1794 2373 6.991531 GTGTATATACCCACCAACGGATTTTA 59.008 38.462 10.38 0.00 0.00 1.52
1795 2374 5.824097 GTGTATATACCCACCAACGGATTTT 59.176 40.000 10.38 0.00 0.00 1.82
1796 2375 5.131475 AGTGTATATACCCACCAACGGATTT 59.869 40.000 10.38 0.00 31.88 2.17
1797 2376 4.657039 AGTGTATATACCCACCAACGGATT 59.343 41.667 10.38 0.00 31.88 3.01
1798 2377 4.039973 CAGTGTATATACCCACCAACGGAT 59.960 45.833 10.38 0.00 31.88 4.18
1799 2378 3.385433 CAGTGTATATACCCACCAACGGA 59.615 47.826 10.38 0.00 31.88 4.69
1800 2379 3.385433 TCAGTGTATATACCCACCAACGG 59.615 47.826 10.38 2.18 31.88 4.44
1801 2380 4.098960 AGTCAGTGTATATACCCACCAACG 59.901 45.833 10.38 0.00 31.88 4.10
1804 2383 3.386726 GCAGTCAGTGTATATACCCACCA 59.613 47.826 10.38 0.00 31.88 4.17
1823 2402 2.228138 AATGCTTGTGGTGTTTGCAG 57.772 45.000 0.00 0.00 37.07 4.41
1826 2405 6.074356 GCTTAGTTTAATGCTTGTGGTGTTTG 60.074 38.462 0.00 0.00 0.00 2.93
1830 2409 5.156355 CAGCTTAGTTTAATGCTTGTGGTG 58.844 41.667 0.00 0.00 33.03 4.17
1837 2416 8.097662 AGTCTAGAAACAGCTTAGTTTAATGCT 58.902 33.333 2.40 0.00 41.48 3.79
1838 2417 8.171840 CAGTCTAGAAACAGCTTAGTTTAATGC 58.828 37.037 2.40 0.00 41.48 3.56
1851 2430 4.697352 CCCATTGGAACAGTCTAGAAACAG 59.303 45.833 3.62 0.00 42.39 3.16
1879 2458 1.202099 TGGGCCCGGATGAAGTAACA 61.202 55.000 19.37 0.00 0.00 2.41
1900 2479 8.538701 AGAGTATTTCCTGCTATCAGATAATGG 58.461 37.037 0.00 0.00 42.95 3.16
1914 2493 6.820656 ACAACTCATAAGCAGAGTATTTCCTG 59.179 38.462 0.00 0.00 45.11 3.86
1929 2508 8.394971 ACAAGATTGATTGTCACAACTCATAA 57.605 30.769 0.00 0.00 39.13 1.90
1930 2509 7.984422 ACAAGATTGATTGTCACAACTCATA 57.016 32.000 0.00 0.00 39.13 2.15
1931 2510 6.889301 ACAAGATTGATTGTCACAACTCAT 57.111 33.333 0.00 0.00 39.13 2.90
2036 2621 6.695292 ATTTGTTTTCTTCATCGCAATGTC 57.305 33.333 0.00 0.00 34.32 3.06
2043 2628 6.076607 GCGAATCGTATTTGTTTTCTTCATCG 60.077 38.462 4.07 0.00 0.00 3.84
2178 2763 6.589135 TGATCTGCATATCAACAATCTGAGT 58.411 36.000 12.01 0.00 32.97 3.41
2214 2799 7.716799 ATGATTTGGCACCTTTACAAAGATA 57.283 32.000 3.25 0.00 37.50 1.98
2262 2851 6.353323 TGTAACACTCTTGAATCCAGACAAA 58.647 36.000 0.00 0.00 0.00 2.83
2315 2905 6.961359 TTGTACAAGATAGATTTCCACACG 57.039 37.500 3.59 0.00 0.00 4.49
2336 2927 0.393537 AGAGCTCGGAAGGCCAATTG 60.394 55.000 5.01 0.00 0.00 2.32
2348 2939 6.327154 TCTCTCGTAATATCTCTAGAGCTCG 58.673 44.000 15.35 11.82 32.38 5.03
2381 2974 6.038161 TCAAAACAATCTTATAGCATGGTCCG 59.962 38.462 0.00 0.00 0.00 4.79
2387 2980 9.113838 CCTACACTCAAAACAATCTTATAGCAT 57.886 33.333 0.00 0.00 0.00 3.79
2388 2981 7.552687 CCCTACACTCAAAACAATCTTATAGCA 59.447 37.037 0.00 0.00 0.00 3.49
2416 3009 7.125811 ACTGGATTCTAACAGCCATAAAGTCTA 59.874 37.037 0.00 0.00 38.25 2.59
2457 3050 3.135167 TGTCATCTGATATGCTGCCTTCA 59.865 43.478 0.00 0.00 0.00 3.02
2475 3068 5.589452 AGCCAAGCAAAATTTTGAATTGTCA 59.411 32.000 30.40 0.00 40.55 3.58
2480 3073 5.124645 TGACAGCCAAGCAAAATTTTGAAT 58.875 33.333 30.40 16.95 40.55 2.57
2564 3157 2.480419 ACAGTGTTTGCGATAACAGCTC 59.520 45.455 3.39 0.00 38.60 4.09
2613 3206 4.261801 GGTGTACATGGACATACAAGCTT 58.738 43.478 15.33 0.00 33.23 3.74
2634 3227 2.366916 AGGTAGCAATCTCATTCTCCGG 59.633 50.000 0.00 0.00 0.00 5.14


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.